A differential thermal model for simulation of Stirling engines was presented. In the new model polytropic expansion/compression processes were substituted to traditional isothermal or adiabatic models of previous studies. In addition, the developed polytropic model was corrected for various loss mechanisms of real engines. In this regard, the effect of non-ideal operation as well as heat recovery in the regenerator was considered. In addition, non-ideal heat transfer of heater and cooler were implemented into the model. In pressure analysis and evaluating work produced or consumed in cylinders, the effect of finite speed motion of piston was considered based the concept of finite speed thermodynamics. Moreover, the effects of heat leakage in regenerator, leakage effect and shuttle effect were evaluated. Finally, new differential polytropic model were employed on a benchmark Stirling engine so-called GPU-3 and accuracy of models was validated through comparing with experimental results as well as previous models. As thermal performance of Stirling engines are significantly affected by thermohydraulic performance of regenerator in one hand and there are various thermohydraulic models for regenerator, three famous thermohydraulic models of regenerator was integrated into models and through comparison with experimental performance of GPU-3 engine, a more accurate thermohydraulic model was introduced.